MolNFT v1 · #87704 · protein
Crystal structure of the strawberry pathogenesis-related 10 (pr-10) fra a 3 protein in complex with catechin
4C94 · Fra a 3 allergen: “Crystal structure of the strawberry pathogenesis-related 10 (pr-10) fra a 3 protein in complex with catechin”. X-ray diffraction, 1 ligand (KXN), 6 pockets (best druggability 0.86). MolNFT v1 #87704 on GenesisL1…
- PDB
- 4C94
- Type
- protein
- Length
- 800 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fra a 3 allergen
- UniProt
- D0E0C7
- Ligands
- KXN
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E | Fra a 3 allergen | protein | 161 | 28% helix, 42% strand | D0E0C7 |
| D | Fra a 3 allergen | protein | 156 | 27% helix, 43% strand | D0E0C7 |
Ligands and binding sites
- KXN · (2R,3S)-2-(3,4-dihydroxyphenyl)-3,4-dihydro-2H-chromene-3,5,7-triol · ligand · 6 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.86 | 0.87 | 110 | KXN |
| 2 | 1138 | 0.84 | 0.85 | 114 | KXN |
| 3 | 304 | 0.74 | 0.86 | 43 | KXN |
| 4 | 193 | 0.52 | 0.77 | 30 | empty |
| 5 | 103 | 0.40 | 0.76 | 19 | empty |
Interfaces
6 interfaces between chains.
- A–B · 782 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 758 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 602 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 337 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 324 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4C94 · Crystal Structure of the Strawberry Pathogenesis-Related 10 (PR-10) Fra a 3 protein in… · the same entry in another collection · chain E against E, TM-score 1.00
- D0E0C7 · AlphaFold monomer V2.0 prediction for major strawberry allergen fra a 1-3 (D0E0C7) · a predicted model of the same protein · chain D against A, TM-score 0.96
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt D0E0C7
- Elsewhere: RCSB PDB 4C94 · PDBe 4C94 · UniProt D0E0C7
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